How To Install rsem on Debian 9
Introduction
In this tutorial we learn how to install rsem on Debian 9.
What is rsem
rsem is:
RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels. For visualization, It can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate. Genomic-coordinate files can be visualized by both UCSC Genome browser and Broad Institute??s Integrative Genomics Viewer (IGV). Transcript-coordinate files can be visualized by IGV. RSEM also has its own scripts to generate transcript read depth plots in pdf format. The unique feature of RSEM is, the read depth plots can be stacked, with read depth contributed to unique reads shown in black and contributed to multi-reads shown in red. In addition, models learned from data can also be visualized. Last but not least, RSEM contains a simulator.
There are three methods to install rsem on Debian 9. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install rsem Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install rsem using apt-get by running the following command:
sudo apt-get -y install rsem
Install rsem Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install rsem using apt by running the following command:
sudo apt -y install rsem
Install rsem Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Debian. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install rsem using aptitude by running the following command:
sudo aptitude -y install rsem
How To Uninstall rsem on Debian 9
To uninstall only the rsem package we can use the following command:
sudo apt-get remove rsem
Uninstall rsem And Its Dependencies
To uninstall rsem and its dependencies that are no longer needed by Debian 9, we can use the command below:
sudo apt-get -y autoremove rsem
Remove rsem Configurations and Data
To remove rsem configuration and data from Debian 9 we can use the following command:
sudo apt-get -y purge rsem
Remove rsem configuration, data, and all of its dependencies
We can use the following command to remove rsem configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge rsem
Dependencies
rsem have the following dependencies:
References
Summary
In this tutorial we learn how to install rsem package on Debian 9 using different package management tools: apt, apt-get and aptitude.